Compositions and Methods for Altering Gene Expression

ABSTRACT

Compositions and methods for regulating gene expression in a growing animal are disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No. 60/891,171, filed on Feb. 22, 2007, the contents of which are incorporated herein by reference.

FIELD OF THE INVENTION

The present invention relates to compositions and methods regulating gene expression or transcription in a growing animal.

BACKGROUND OF THE INVENTION

Commercially available canine and feline foods include compositions specially formulated to address many different nutritional needs. These include, for example, formulations designed for different breed types, sizes and body conditions. They also include formulations designed to address the nutritional needs of animals in the different stages of their life cycle. Typically, these stages include the growth, adult and senior stages of life. For example, U.S. Pat. No. 5,851,573 discloses a pet food composition for large breed puppies; U.S. Pat. No. 6,426,100 discloses compositions to provide improved bone modeling and chondrocyte functioning in growing animals; U.S. Pat. No. 6,582,752 discloses gender specific puppy food. Despite the availability of such pet food formulations, however, the need remains for the development of additional formulations comprising innovative ingredients and nutrients designed to enhance the development of growing animals.

It is known in the art that certain nutrients have an effect on gene expression. Nutrigenomics is the study of such a relationship. Despite what is already known, there is a need to develop compositions and methods which may positively influence gene expression of an animal.

SUMMARY OF THE INVENTION

In certain aspects, the present invention relates to compositions that are useful to enhance the development of a growing animal. Particularly, the compositions of the present invention comprise one or more nutrients or bioactive substances that can enhance neurologic development, bone and joint health, immune function, and promote healthy body composition in a growing animal. In certain embodiments, the nutrients and bioactive substances include, but are not limited to, fatty acids, antioxidants, essential nutrients, amino acids, minerals and trace elements, vitamins and vitamin-like substances. Other aspects of the invention relate to methods to enhance the development of a growing animal comprising administration of effective amounts of the compositions of the present invention directly to a growing animal or to the dam of said animal while the animal is in utero or is a nursling.

Thus, in one aspect, the present invention includes Composition 1.0, a pet food composition comprising:

about 5 to about 70% protein,

about 0.5 to about 1.6% methionine,

about 50 to about 200 ppm manganese,

about 0.1 to about 0.5% DHA,

about 0.1 to about 0.7% EPA,

about 1200 to about 7500 ppm choline,

about 1000 to about 2000 ppm taurine,

about 2.5 to about 6% linoleic acid,

about 1 to about 3% total n-3 fatty acids,

about 50 to about 1200 IU/kg vitamin E,

about 50 to about 500 ppm vitamin C,

about 50 to about 500 ppm carnitine, and

about 2.5 to about 7 g lysine/1000 kcal.

The preset invention also includes the following compositions:

1.1 Composition 1.0 comprising:

-   -   0 to about 90% by weight of carbohydrates;     -   about 20% to about 60% by weight of protein;     -   about 2% to about 50% by weight of fat;     -   about 0.1% to about 20%, by weight of total dietary fiber; and     -   0 to about 15% by weight of vitamins, minerals, and other         nutrients in varying percentages which support the nutritional         needs of the animal.         1.2 Composition 1.0 or 1.1 comprising about 5% to about 55%, by         weight of carbohydrates;         1.3 Any of the preceding compositions comprising about 20% to         about 50%, by weight of protein, e.g., about 22% to about 50%;         1.4 Any of the preceding compositions comprising about 5% to         about 40%, by weight of fat, e.g., e.g., at least about 8% or         about 9% to about 40% fat;         1.5 Any of the preceding compositions comprising about 1% to         about 11%, by weight of total dietary fiber;         1.6 Any of the preceding compositions comprising about 0.1% to         about 0.4% DHA, e.g., about 0.5%; 61.7 Any of the preceding         compositions comprising about 200 IU/kg to about 1200 IU/kg         Vitamin E, e.g., about 200 IU/kg to about 1000 IU/kg;         1.9 Any of the preceding compositions comprising about 100 ppm         to about 500 ppm carnitine, e.g., about 200 to about 400, or         about 300 ppm;         1.10 Any of the preceding compositions comprising about 2.5         g/1000 kcal to about 7 g/1000 kcal lysine;         1.11 Any of the preceding compositions comprising about 2500 ppm         to about 7500 ppm choline, e.g., about 3000, about 3500, about         4000, about 4500, about 4600, about 4625, about 4650, about         4700, about 4800, or about 6000 ppm;         1.12 Any of the preceding compositions comprising about 0.1% to         about 0.6% EPA;         1.13 Any of the preceding compositions comprising about 50 ppm         to about 150 ppm manganese; and         1.14 Any of the preceding compositions comprising about 0.8% to         about 1.6% methionine.

In another aspect, the invention relates to methods to cause a beneficial modification in gene expression in an animal, specifically, down regulation in expression of a gene or genes associated with an undesirable biological condition or pathway or disease state and/or up regulation in expression of a gene or genes associated with a desired biological condition or pathway or which may have a positive or preventive effect on a disease state for any one or more biological conditions, pathways or disease states and genes described in Tables 2-15, comprising administering an effective amount of a composition of according to any one of compositions 1.0-1.14 to an animal, either directly to the animal or to the dam while the animal is in utero.

In another aspect, the invention is directed to Method 2.0, a method to regulate gene expression in a canine comprising administering to the canine any one of compositions the compositions of the present invention, e.g., compositions 1.0-1.14.

The present invention also includes the following methods:

-   -   2.1 Of method 2.0 wherein the canine is a puppy.     -   2.2 Of method 2.0 or 2.1 wherein the canine is born of a dam fed         any one of compositions 1.0-1.14 during pregnancy.     -   2.3 Of method 2.2 wherein the puppy is in utero.     -   2.4 Of method 2.2 wherein the dam is fed any one of compositions         1.0-1.14 prior to pregnancy.     -   2.5 Of method 2.2 or 2.4 wherein the dam is fed any one of         compositions 1.0-1.14 for a majority of the pregnancy duration.     -   2.6 Of any one of methods 2.2-2.5 wherein the dam is fed         compositions consisting essentially of any one of compositions         1.0-1.14 prior to and during pregnancy.     -   2.7 Of any one of the preceding methods wherein the puppy is fed         any one of compositions 1.0-1.14 prior to weaning, e.g., while         still a nursling.     -   2.8 Of any one of the preceding methods wherein the puppy is fed         any one of compositions 1.0-1.14 post weaning.     -   2.9 Of method 2.8 wherein the puppy is fed food compositions         consisting of any one of compositions 1.0-1.14.     -   2.10 Of any one of the preceding methods wherein an effective         amount of the composition is administered to the canine.     -   2.11 Of any one of the preceding methods wherein the composition         is administered to the canine for an effective amount of time.     -   2.12 Of method 2.11 wherein the composition is administered to         the canine for at least one year post partum or one year post         weaning.     -   2.13 Of any one of the preceding method wherein the gene is         selected from those listed in Tables 2-15.

In a further aspects, the invention relates to the use of any of the formulae of the present invention in the manufacture of a composition to modify gene expression in an animal as described herein.

Other features and advantages of the present invention will be understood by reference to the detailed description of the examples that follow.

DETAILED DESCRIPTION OF THE INVENTION

It is contemplated that the invention described herein is not limited to the particular methodology, protocols, and reagents described as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention in any way.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. In addition, all references cited herein are hereby incorporated by reference in their entireties. In the event of a conflict in a definition in the present disclosure and that of a cited reference, the present disclosure controls.

As used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise.

The present invention relates to any animal, preferably a mammal, more preferably a companion animal. The term “companion animal” refers to any animal that lives in close association with humans and includes, but is not limited to, canines and felines of any breed. It is contemplated herein, however, that any animal whose diet may be controlled by humans may benefit from feeding the formulations disclosed herein. These animals may include, for example, domesticated farm animals (e.g., cattle, horses, swine, etc.) as well as undomesticated animals held in captivity, e.g., in zoological parks and the like. Preferred animals include canines, e.g., dogs, including growing dogs, e.g., puppies.

“Beneficial modification in the expression of genes” as used herein includes, e.g., down regulation of genes expressing proteins associated with disease states and/or up regulation of genes expressing proteins which have a beneficial or healthful effect as compared to appropriate controls, as may be determined using conventional methods, e.g., by microarray (e.g., Affymetrix gene chip) techniques familiar to one of skill in the art. Further, one of skill in the art is familiar with the known associations between diseases and specific genes as those listed in the tables provided hereinbelow such that it is understood whether an increase or decrease in expression of a particular gene is desirable.

The “growth” life stage of an animal refers to the period from birth or weaning (approximately 8 weeks of age) to about 1 year of age or beyond, depending on the species and breed of the animal.

As used herein, the term “puppy” refers to an immature canine, typically between the ages of birth and 12 months.

“Essential amino acids” as used herein refers to those amino acids that cannot be synthesized de novo by an organism and thus must be supplied in the diet. It is understood by one of skill in the art that the essential amino acids varies from species to species, depending upon the organism's metabolism. For example, it is generally understood that the essential amino acids for dogs and cats (and humans), are phenylalanine, leucine, methionine, lysine, isoleucine, valine, threonine, tryptophan, histidine and arginine.

As understood by one of skill in the art, a “limiting amino acid” refers to an amino acid which if present in insufficient quantities in a diet, results in the limitation in usefulness of other essential amino acids, even if the other essential amino acids are present in otherwise large enough quantities. Lysine is the limiting essential amino acid in the compositions disclosed herein. Thus, the remaining essential amino acids are quantitatively formulated or “balanced” in relationship to the amount of lysine determined critical to affect the desired biological result. As used herein, “balanced amino acids” refers to the relationship of the essential amino acid lysine to energy to assure optimal animal growth and development.

“Essential nutrients” as used herein refers to nutrients required for normal body functioning that cannot be synthesized by the body. Categories of essential nutrient include vitamin dietary minerals, fatty acid, and amino acid. It is understood by one of skill in the art that the nutrients deemed essential varies from species to species, depending upon the organism's metabolism. For example, essential nutrients for dogs and cats include Vitamins A, D, E, K, B1, B6 B12, riboflavin, niacin, pantothenic acid, folic acid, calcium, phosphorous, magnesium, sodium, potassium, chlorine, iron, copper, zinc, manganese, selenium and iodine. Choline, generally regarded as a B complex vitamin, may be included among the semi-essential nutrients. In addition, taurine, while technically not an amino acid but a derivative of cysteine, is an essential nutrient for cats.

Carnitine, also known as L-carnitine, (levocarnitine) is a quaternary ammonium compound synthesized from the amino acids lysine and methionine and is responsible for the transport of fatty acids from the cytosol into the mitochondria.

Without being limited to any theories or particular modes of action, the present invention is based on the surprising discovery that the addition of certain ingredients to pet food compositions and administration of these compositions to animals can enhance the development of a growing animal. For example, data indicate that animals fed the compositions of the present invention (or those whose dams were fed the compositions during gestation and prior to weaning but continued throughout growth of their litters), demonstrate enhanced neurologic development, bone and joint health, immune function, and have overall healthier body composition. Interestingly, microarray data also indicate a differential change in gene expression in these animals compared to controls which is generally reflective of a beneficial modification (i.e., up or down regulation) in the expression of many genes associated with biological processes including those involved in growth and development. Thus, in one aspect, the invention relates to compositions and methods to enhance the development of a growing animal as described in detail herein.

As contemplated herein, the compositions of the present invention comprise nutritionally complete and balanced animal feed compositions. Such compositions include, among other nutrients and ingredients, recommended healthful amounts of protein, carbohydrate and fat. “Nutritionally complete and balanced animal feed compositions”, as well as nutrients and ingredients suitable for animal feed compositions, and recommended amounts thereof, are familiar to one of skill in the art (see, for example, National Research Council, 2006 Nutritional Requirements for Dogs and Cats, National Academy Press, Washington D.C. or the Official Publication of the Association of American Feed Control Officials, Inc. Nutrient Requirements for Dogs and Cats 2006).

It is contemplated herein that the compositions disclosed herein may also comprise antioxidants, additives, stabilizers, thickeners, flavorants, palatability enhancers and colorants in amounts and combinations familiar to one of skill in the art. “Antioxidants” refers to a substance that is capable of reacting with or decreasing the production of free radicals and neutralizing them. Examples include, but are not limited to, beta-carotene, selenium, coenzyme Q10 (ubiquinone), lutein, tocotrienols, soy isoflavones, S-adenosylmethionine, glutathione, taurine, N-acetylcysteine, vitamin E, vitamin D, vitamin C, flavanoids, anthocyanindins, and lipoic acid.

While foods of any consistency or moisture content are contemplated, preferably the compositions of the present invention may be, for example, a wet, semi-dry, or dry animal food composition. “Wet” food refers to food which is sold in cans or foil bags and has a moisture content of about 70 to about a 90%. “Dry” food refers to compositions with about 5 to about 15% moisture content and is often manufactured in the form of small bits or kibbles. Semi-dry compositions refers to food which has a moisture content greater than dry foods, but less than wet foods. Also contemplated herein are compositions of intermediate moisture consistency and those that may comprise components of various consistency as well as components that may include more than one consistency, for example, soft, chewy meat-like particles as well as kibble having an outer cereal component and an inner cream component as described in, e.g., U.S. Pat. No. 6,517,877.

Various processes for manufacturing and packaging the compositions of the present invention may be employed and are familiar to one of skill in the art.

It is also contemplated herein that the methods of the present invention include methods to cause a beneficial modification in gene expression in an animal, specifically, down regulation in expression of a gene or genes associated with an undesirable biological condition or pathway or disease state and/or up regulation in expression of a gene or genes associated with a desired biological condition or pathway or which may have a positive or preventive effect on a disease state, as the case may be, for any one or more biological conditions, pathways or disease states and genes described in Tables 14-27, comprising administering an effective amount of a composition of the present invention to the animal, either directly to the animal or to the dam while the animal is in utero. Indeed, as discussed in Examples 7 and 8 here-in-below, by effecting the animal at the genomic level, the administration of the compositions of the present invention, either directly to the animal or to the dam while the animal is in utero, may have beneficial, even prophylatic, health effects on the animal by effecting the expression of any one or more genes listed in Tables 14-27. For example, the administration of an effective amount of a composition of the present invention to an animal may enhance bone and joint health in the animal by causing the down regulation in genes associated with cartilage and joint damage associated with arthritis, e.g. interleukin 1-beta, fibronectin, lactoransferrin, etc. (see Table 14).

It is contemplated herein that the compositions of the present invention may be administered to an animal alone as a complete nutritionally balanced diet, or in conjunction with dietary supplements, vitamins and/or other nutritionally beneficial agents familiar to one of skill in the art, as part of an overall wellness program for the animal. Compositions of the invention may also be useful as a veterinary therapeutic product. As such, the compositions may optionally contain a carrier, diluent, or an excipient, the suitability of which for the intended use being familiar to one of skill in the art.

It is also contemplated that, in addition to administering the compositions disclosed herein directly to a growing animal, e.g., to a growing puppy or kitten, the compositions may be administered to the dam of the animal while the animal is still in utero or while the animal is a nursling.

The following examples further illustrate the present invention and are not intended to limit the invention. As used throughout, ranges are used as shorthand for describing each and every value that is within the range. Any value within the range can be selected as the terminus of the range. It is understood that when formulations are described, they may be described in terms of their ingredients, as is common in the art, notwithstanding that these ingredients may react with one another in the actual formulation as it is made, stored and used, and such products are intended to be covered by the formulations described.

The following examples further describe and demonstrate illustrative embodiments within the scope of the present invention. The examples are given solely for illustration and are not to be construed as limitations of this invention as many variations are possible without departing from the spirit and scope thereof. Various modifications of the invention in addition to those shown and described herein should be apparent to those skilled in the art and are intended to fall within the appended claims.

Except to the extent stated otherwise, all percentages used in this specification are weight percentages on a dry matter basis. The phrase “dry matter basis” means the component concentration in the composition after any moisture in the composition is removed.

EXAMPLES Example 1 Canine Genetic Effects: Conception to One Year of Age

In order to characterize the genotypic effects of feeding a composition formulated to enhance the development of a growing animal, an experiment is performed to identify changes in gene expression in puppies at one year of age from dams fed the compositions disclosed in Table 1.

TABLE 1 Average of analyzed nutrient profiles of foods utilized in the study Nutrients, 100% Dry Matter Basis Composition H Composition P Moisture, % 6.09 7.44 Crude Protein, % 29.4 27.9 Fat, % 17.6 14.2 Ca, % 1.43 1.46 P, % 1.2 0.96 EPA, % 0.31 <0.01 DHA % 0.19 0.01 Linoleic Acid, % 3.8 2.14 Total n-3 fatty acids, % 1.4 0.19 Total n-6 fatty acids, % 3.7 2.6 Taurine, % 0.14 0.08 Carnitine, ppm 312.1 No analysis Methionine, % 1.3 0.52 Cystine, % 0.4 0.39 Manganese, % 94.5 64 Vitamin E, IU/kg 816 43.8 Vitamin C, ppm 168.6 <10 Choline, ppm 4876 No analysis

Composition P is a commercially available dog food. Composition H is an experimental dog food composition.

Dams are fed either Composition H or Composition P for at least 10 days prior to conception. Dams are maintained in group lodging until confirmed pregnant via palpation, and are then moved to maternity lodging. Puppies from dams are kept on the same foods fed to the dams until one year of age (including pre-weaning and post-weaning period). Blood samples are then taken from the puppies and mRNA isolated according to conventional methods. Microarray assays are performed using the Affymetrix Canine-2 gene chip according to conventional methods.

The tables below show the genes grouped by function and the direction of expression, wherein up regulation in Composition H (“H”) vs Composition P (“P”) demonstrates increased gene expression in Composition H fed puppies compared to Composition P fed puppies. Similarly, down regulation of a gene in the Composition H fed puppies vs Composition P fed puppies represents decreased gene expression in puppies fed Composition H relative to those fed Composition P.

TABLE 2 Genes associated with arthritis/inflammation relevant to bone and joints Direction of expression Annotation Probe H vs P Interleukin 1-beta CfaAffx.11741.1.S1_s_at down Fibronectin Cfa.3707.1.A1_s_at down v-fos FBJ murine osteo- Cfa.9039.1.A1_at down sarcoma viral oncogene homolog dual specificity phosphatase 1 CfaAffx.25714.1.S1_s_at down Lactotransferrin CfaAffx.21286.1.S1_s_at down compliment component 5a CfaAffx.7180.1.S1_s_at down receptor xanthine dehydrogenase CfaAffx.9452.1.S1_s_at down Secreted phoshoprotein 1 CfaAffx.15042.1.S1_s_at down

TABLE 3 Genes associated with DNA replication and repair Direction of expression Annotation Probe H vs P DNA fragmentation Interleukin 1-beta CfaAffx.11741.1.S1_s_at down Fibronectin Cfa.3707.1.A1_s_at down Neuroregulin 1 CfaAffx.10523.1.S1_s_at down Dual specificity phosphatase 1 CfaAffx.25714.1.S1_s_at down Cell death-inducing DFFA- CfaAffx.28752.1.S1_at down like effector a Proper DNA processing control Budding uninhibited by Cfa.1559.1.A1_at up benzimidazoles 1 homolog Topoisomerase II alpha Cfa.18946.1.S1_s_at up Kinetochore associated 2 Cfa.3066.1.S1_s_at up Claspin homolog CfaAffx.6235.1.S1_s_at up Cyclin B1 CfaAffx.12419.1.S1_s_at up Cyclin B2 Cfa.11939.1.A1_s_at up Human chromosome CfaAffx.25509.1.S1_at up condensation protein G Leucine zipper protein 5 CfaAffx.8781.1.S1_s_at up Kinesin family member 23 Cfa.15293.1.A1_at up Flap structure specific Cfa.1854.1.A1_at up endonuclease 1

TABLE 4 Genes associated with cancer Direction of expression Annotation Probe H vs P Interleukin 1-beta CfaAffx.11741.1.S1_s_at down Fibronectin Cfa.3707.1.A1_s_at down v-fos FBJ murine osteosarcoma viral oncogene Cfa.9039.1.A1_at down homolog dual specificity phosphatase 1 CfaAffx.25714.1.S1_s_at down compliment component 5a receptor CfaAffx.7180.1.S1_s_at down xanthine dehydrogenase CfaAffx.9452.1.S1_s_at down cellular repressor of E1A-stimulated genes 1 Cfa.10558.3.A1_at down chondroitin sulfate proteoglycan 2 CfaAffx.13597.1.S1_s_at down transcobalamin II, mycrocytic anemia CfaAffx.19852.1.S1_s_at down serpin peptidase inhibitor, clade B member 10 CfaAffx.1043.1.S1_s_at down adenomatosis polyposis coli down-regulated 1 CfaAffx.28621.1.S1_at down six membrane epithelial antigen of the prostate 2 Cfa.1933.1.S1_at down alanyl aminopeptidase Cfa.3774.1.A1_s_at down Cancer susceptibility candidate 5 Cfa.1126.1.S1_at up Paternally expressed 3 Cfa.4482.1.S1_at up Topoisomerase II alpha Cfa.18946.1.S1_s_at up Tubulin alpha 6 CfaAffx.13667.1.S1_at up Cyclin B1 CfaAffx.12419.1.S1_s_at up Cell division cycle associated 1 CfaAffx.20529.1.S1_at up Cell division cycle 2 CfaAffx.20006.1.S1_at up Ribonucleotide reductase M2 polypeptide CfaAffx.6059.1.S1_at up Breast cancer anti-estrogen resistance 3 Cfa.651.1.S1_at up Tumor necrosis factor receptor superfamily CfaAffx.28790.1.S1_at up member 17 Protein kinase C, iota CfaAffx.22822.1.S1_s_at up

TABLE 5 Genes associated with cell compromise Direction of expression Annotation Probe H vs P Interleukin 1-beta CfaAffx.11741.1.S1_s_at down Fibronectin Cfa.3707.1.A1_s_at down Neuroregulin 1 CfaAffx.10523.1.S1_s_at down v-fos FBJ murine osteo- Cfa.9039.1.A1_at down sarcoma viral oncogene homolog dual specificity phosphatase 1 CfaAffx.25714.1.S1_s_at down compliment component 5a CfaAffx.7180.1.S1_s_at down receptor xanthine dehydrogenase CfaAffx.9452.1.S1_s_at down Macrophage receptor with Cfa.15713.1.A1_s_at down collagenous structure Cyclin B1 CfaAffx.12419.1.S1_s_at up Cell division cycle 2 CfaAffx.20006.1.S1_at up Hemoglobin epsilon 1 CfaAffx.10240.1.S1_s_at up Protein kinase C, iota CfaAffx.22822.1.S1_s_at up

TABLE 6 Genes associated with cellular assembly Direction of expression Annotation Probe H vs P Interleukin 1-beta CfaAffx.11741.1.S1_s_at down Fibronectin Cfa.3707.1.A1_s_at down Neuroregulin 1 CfaAffx.10523.1.S1_s_at down chondroitin sulfate CfaAffx.13597.1.S1_s_at down proteoglycan 2 cholinergic receptor, Cfa.8414.1.A1_s_at down muscarinic 3 xanthine dehydrogenase CfaAffx.9452.1.S1_s_at down Macrophage receptor with Cfa.15713.1.A1_s_at down collagenous structure Cyclin B1 CfaAffx.12419.1.S1_s_at up Cell division cycle 2 CfaAffx.20006.1.S1_at up Leucine zipper protein 5 CfaAffx.8781.1.S1_s_at up Protein kinase C, iota CfaAffx.22822.1.S1_s_at up Kinesin family member 23 Cfa.15293.1.A1_at up Budding uninhibited by Cfa.1559.1.A1_at up benzimidazoles 1 homolog Cyclin B2 Cfa.11939.1.A1_s_at up Topoisomerase II alpha Cfa.18946.1.S1_s_at up Kinetochore associated 2 Cfa.3066.1.S1_s_at up Cell division cycle CfaAffx.20529.1.S1_at up associated 1 Human chromosome CfaAffx.25509.1.S1_at up condensation protein G Kinesin family member 11 CfaAffx.12118.1.S1_s_at up A kinase (PRKA) anchor Cfa.10574.1.A1_at up protein 2 thymopioten Cfa.18367.2.S1_s_at up

TABLE 7 Genes associated with cell cycle regulation Direction of expression Annotation Probe H vs P Interleukin 1-beta CfaAffx.11741.1.S1_s_at down Fibronectin Cfa.3707.1.A1_s_at down Neuroregulin 1 CfaAffx.10523.1.S1_s_at down v-fos FBJ murine osteosarcoma viral oncogene Cfa.9039.1.A1_at down homolog cholinergic receptor, muscarinic 3 Cfa.8414.1.A1_s_at down dual specificity phosphatase 1 CfaAffx.25714.1.S1_s_at down cellular repressor of E1A-stimulated genes 1 Cfa.10558.3.A1_at down Cyclin B1 CfaAffx.12419.1.S1_s_at up Cell division cycle 2 CfaAffx.20006.1.S1_at up Leucine zipper protein 5 CfaAffx.8781.1.S1_s_at up centromere protein F, 350/400ka (mitosin) CfaAffx.19534.1.S1_at up Breast cancer anti-estrogen resistance 3 Cfa.651.1.S1_at up Budding uninhibited by benzimidazoles 1 Cfa.1559.1.A1_at up homolog Cyclin B2 Cfa.11939.1.A1_s_at up Topoisomerase II alpha Cfa.18946.1.S1_s_at up Kinetochore associated 2 Cfa.3066.1.S1_s_at up Cell division cycle associated 1 CfaAffx.20529.1.S1_at up Human chromosome condensation protein G CfaAffx.25509.1.S1_at up Kinesin family member 11 CfaAffx.12118.1.S1_s_at up thymopioten Cfa.18367.2.S1_s_at up

TABLE 8 Genes associated with various functions Direction of expression Annotation Probe H vs P calcyphosine-like Cfa.21214.1.S1_s_at down ELKS/RAB6 interacting/CAST family member 2 Cfa.21214.1.S1_at down glutamyl tRNA synthetase 2 Cfa.2057.1.A1_at down Coiled-coil containing domain 3 Cfa.9084.1.A1_at down chromosome 16 clone RP11-26P10 Cfa.3834.1.S1_at down SAM domain- and HD domain-containing CfaAffx.13689.1.S1_at down protein 1 AJ420591 Cfa.15196.1.A1_at down family with sequence similarity 46, member A CfaAffx.5194.1.S1_at down CD1a antigen Cfa.18390.1.S1_s_at down epidermal dendritic cell marker (CD1a) CfaAffx.17796.1.S1_at down ANKYRIN MOTIF CfaAffx.6104.1.S1_s_at down RP11-549H3 on chromosome X Cfa.9597.1.S1_at down La ribonucleoprotein domain family, member 1 Cfa.14608.1.A1_at down adenomatosis polyposis coli down-regulated 1 CfaAffx.28621.1.S1_at down Chromosome 3 open reading frame 21 CfaAffx.20763.1.S1_at down EGF-like module containing, mucin-like, CfaAffx.28381.1.S1_s_at down hormone receptor-like 1 acyltransferase like 1 CfaAffx.14833.1.S1_at down RP11-95J15 from 7 Cfa.6138.1.A1_at down CD8 antigen, beta polypeptide 2 Cfa.21011.1.S1_at down multimerin 1 CfaAffx.15515.1.S1_s_at down none Cfa.12500.1.A1_at down Hypothetical protein FLJ21062 Cfa.1933.2.A1_at down normal mucosa of esophagus specific 1 Cfa.11815.1.A1_at down regulator of G-protein signalling 7 CfaAffx.24021.1.S1_s_at down Islet cell auto-antigen 1 Cfa.11691.1.A1_at down normal mucosa of esophagus specific 1 (NMES1), CfaAffx.851.1.S1_s_at down transcript variant 2 none Cfa.5989.1.A1_s_at down eukaryotic translation initiation factor 2, subunit Cfa.9060.1.A1_at down 3 gamma Serine/threonine kinase 17A CfaAffx.21987.1.S1_at down RP11-542F9 on chromosome 6 CfaAffx.21067.1.S1_at up chromosome 20 open reading frame 172 CfaAffx.13625.1.S1_at up RP11-111I12 on chromosome 1 CfaAffx.16431.1.S1_at up BAT2 domain containing 1 Cfa.15064.1.S1_at up Rho GTPase activating protein 11A CfaAffx.13079.1.S1_s_at up polo-like kinase 4 CfaAffx.6762.1.S1_s_at up NADH dehydrogenase (ubiquinone) flavoprotein 3 CfaAffx.16432.1.S1_s_at up 3 BAC RP11-223L18 Cfa.3066.1.S1_at up par-3 partitioning defective 3 homolog B Cfa.12402.1.S1_a_at up Hypothetical protein MGC24039 Cfa.19506.1.S1_at up immunoglobulin mu heavy chain CfaAffx.539.1.S1_x_at up origin recognition complex, subunit 1-like Cfa.8552.1.A1_s_at up RP11-653G16 from 4 CfaAffx.15773.1.S1_at up abnormal spindle-like microcephaly-associated Cfa.103.1.A1_s_at up protein Solute carrier family 22 Cfa.10558.2.S1_at up BCSynL32 immunoglobulin lambda light chain CfaAffx.346.1.S1_at up Purinergic receptor P2Y, G-protein coupled 10 Cfa.1521.1.S1_at up DEP domain containing 1 CfaAffx.31279.1.S1_at up chromosome 17, clone RP11-160L11 Cfa.16355.1.S1_at up Hypothetical protein LOC644115 Cfa.15220.2.A1_at up isolate MRPS17P1 mitochondrial ribosomal Cfa.12402.1.S1_s_at up protein S17 KIAA0101 (L5) CfaAffx.26141.1.S1_s_at up chromosome 13 open reading frame 3 CfaAffx.11656.1.S1_at up SHC SH2-domain binding protein 1 CfaAffx.6499.1.S1_at up CDC20 cell division cycle 20 homolog CfaAffx.8850.1.S1_s_at up Chromosome 14 open reading frame 32 CfaAffx.23135.1.S1_s_at up 3-oxoacyl-ACP synthase, mitochondrial Cfa.10049.1.A1_s_at up MAD2 mitotic arrest deficient-like 1 CfaAffx.25205.1.S1_s_at up thioredoxin domain containing 5 Cfa.10753.1.A1_at up Apla tubulin Cfa.6991.1.A1_at up none CfaAffx.32.1.S1_at up Melanin-concentrating hormone receptor 1 Cfa.6032.1.A1_at up Aquaporin 7 Cfa.21549.1.S1_s_at up cathepsin E CfaAffx.15966.1.S1_at up EF hand domain (C-terminal) containing 2 Cfa.1885.1.A1_at up bone morphogenetic protein 6 Cfa.15702.1.S1_at up hemoglobin, alpha 2 Cfa.3973.2.A1_s_at up SH3-domain GRB2-like 3 Cfa.10644.1.A1_at up Acidic nuclear phosphoprotein 32 family, Cfa.31.1.S1_s_at up member A none CfaAffx.20953.1.S1_x_at up Rh family, B glycoprotein Cfa.13613.1.A1_at up putative protein STRF8 CfaAffx.15063.1.S1_s_at up fatty acid desaturase 1 Cfa.13257.1.A1_at up Ligand dependent nuclear receptor corepressor- Cfa.1476.1.A1_at up like F-box only protein 2 CfaAffx.9335.1.S1_at up Ring finger protein 152 Cfa.15414.1.A1_at up immunoglobulin lambda constant 1 CfaAffx.22878.1.S1_at up G-protein coupled receptor 158 Cfa.9162.1.A1_at up Hypothetical protein MGC42105 CfaAffx.28387.1.S1_at up

Gene expression profiles from puppies fed Composition H and P are obtained and compared. Results indicate that 143 genes are differentially expressed between the study groups and, in general, their functions may be associated with cell assembly, cell cycle regulation, DNA replication and repair, cell compromise, arthritis and cancer. At a minimum of 1.5 fold change, 143 genes are differentially expressed in the two groups.

Genes associated with arthritis/inflammation are down-regulated in puppies fed Composition H compared to puppies fed Composition P, which suggests reduced cartilage/joint damage in Prototype pups. A separate study performed also indicates that levels of bone alkaline phosphatase are lower in puppies fed composition H (data not shown). See Table 2.

Genes associated with DNA fragmentation are down-regulated and genes associated with DNA processing control are up-regulated in puppies fed Composition H compared to puppies fed Composition P, which suggests reduced DNA damage and improved DNA protection in Prototype pups (also supported by elevated Vitamin E levels in blood, data not shown). See Table 3.

Genes associated with cancer incidence are down-regulated and genes associated with tumor suppression are up-regulated in puppies fed Composition H compared to puppies fed Composition P, which suggests the possibility of reduced cancer susceptibility in these Prototype animals; see Table 4.

Genes associated with cellular compromise are down-regulated and genes associated with cellular integrity are up-regulated in puppies fed Composition H compared to puppies fed Composition P, which suggests the possibility of reduced cell damage and enhanced cellular protection in these Prototype animals (also supported by elevated Vitamin E levels in blood, data not shown). See Table 5.

Genes associated with disruption of cellular assembly are down-regulated and genes associated with proper cellular organization are up-regulated in puppies fed Composition H compared to puppies fed Composition P, which suggests improved cellular organization and function in Prototype pups. See Table 6.

Genes associated with proper cell cycle regulation are up-regulated and genes associated with disruption of cell cycle control are down-regulated in puppies fed Composition H compared to puppies fed Composition P, which suggests proper control of cell cycle progression and cell survival. See Table 7.

Thus, it is contemplated herein that the nutritional benefits of the compositions of the present invention as described herein may involve modification in gene expression which results in the enhancement of the development of a growing animal. In addition, feeding proper nutrients during early development may have a prophylatic effect and influence disease processes later in life, i.e., lessen the chance of disease in the animal, as the expression of genes associated with common diseases and disorders may be influenced due to the given nutritional compositions of the foods provided maternally and during early development.

Example 2

An experiment is performed to determine the effects on gene expression in puppies fed Composition H vs. Composition P from weaning until one year of age.

Dams utilized in this study are fed Composition P prior to, and during pregnancy. Following weaning, puppies are divided into two groups and provided with either Composition H or maintained on Composition P until one year old. Blood samples are then taken from the puppies and mRNA isolated according to conventional methods. Microarray assays are performed using the Affymetrix Canine-2 gene chip according to conventional methods.

Results indicate that 99 genes are differentially expressed between the two study groups, and are presented in Tables 9-15. Of the genes identified, many are related to biological functions or pathways such as, e.g., immune activation, lipid metabolism, cardiovascular development, skeletal and muscular disorders, contraction and function and cell compromise and cancer.

TABLE 9 Genes associated with immune activation Direction of expression Annotation Probe H v. P lymphocyte antigen 6 CfaAffx.1839.1.S1_at down complex Fc fragment of IgG, receptor, Cfa.17806.2.S1_s_at up transporter, alpha fibrinogen-like 2 Cfa.10303.1.S1_at down CD1A antigen Cfa.18390.1.S1_s_at down complement factor D (adipsin) Cfa.21381.1.S1_s_at down CD163 antigen; macrophage- Cfa.9647.1.A1_at down associated antigen toll-like receptor 2 CfaAffx.13248.1.S1_s_at down lysozyme (renal amyloidosis) CfaAffx.1598.1.S1_s_at down transcription elongation factor Cfa.12580.1.S1_s_at down A (SII), 3 fibronectin 1 Cfa.3707.2.S1_at down macrophage receptor with Cfa.15713.1.A1_s_at down collagenous structure bactericidal/permeability- CfaAffx.14056.1.S1_s_at down increasing protein T cell receptor alpha locus Cfa.10333.1.A1_at down immunoglobulin heavy Cfa.4556.3.A1_a_at down constant alpha 2 nuclear factor I/B Cfa.4487.1.S1_at up

TABLE 10 Genes associated with Cancer formation Direction of expression Annotation Probe P vs C fibronectin 1 Cfa.3707.3.S1_s_at down xanthine dehydrogenase CfaAffx.9452.1.S1_s_at down neuregulin 1 CfaAffx.10523.1.S1_s_at down colony stimulating factor 1 CfaAffx.27899.1.S1_at down receptor alanyl aminopeptidase Cfa.3774.1.A1_s_at down S100 calcium binding protein CfaAffx.22128.1.S1_at down dystroglycan 1 CfaAffx.17467.1.S1_at up

TABLE 11 Genes associated with Lipid metabolism Direction of expression Annotation Probe H v. P Toll-like receptor 2 CfaAffx.13248.1.S1_s_at Down cytochrome P450, family 1, CfaAffx.10229.1.S1_at Down subfamily B, polypeptide 1 colony stimulating factor 1 CfaAffx.27899.1.S1_at Down receptor phospholipase C, beta 1 Cfa.10853.1.A1_at Down fibronectin 1 Cfa.3707.3.S1_s_at Down neuregulin 1 CfaAffx.10523.1.S1_s_at Down macrophage receptor with Cfa.15713.1.A1_at Down collagenous structure CD1a molecule Cfa.18390.1.S1_s_at Down

TABLE 12 Genes associated with Cardiovascular development Direction of expression Annotation Probe H v. P bactericidal/permeability- CfaAffx.14056.1.S1_s_at Down increasing protein fibronectin 1 Cfa.3707.3.S1_s_at Down neuregulin 1 CfaAffx.10523.1.S1_s_at Down xanthine dehydrogenase CfaAffx.9452.1.S1_s_at Down annexin A6 CfaAffx.27471.1.S1_s_at Down colony stimulating factor 1 CfaAffx.27899.1.S1_at Down receptor alanyl (membrane) Cfa.3774.1.A1_s_at Down aminopeptidase

TABLE 13 Genes associated with Skeletal/Muscular disorders and contraction/function Direction of expression Annotation Probe H v. P Skeletal/Muscular disorders Toll-like receptor 2 CfaAffx.13248.1.S1_s_at down colony stimulating factor 1 CfaAffx.27899.1.S1_at down receptor fibronectin 1 Cfa.3707.3.S1_s_at down neuregulin 1 CfaAffx.10523.1.S1_s_at down Muscle contraction/function exostoses Cfa.11001.1.A1_at up microfibrillar associated CfaAffx.21449.1.S1_s_at up protein 5 myosin light polypeptide Cfa.13192.1.S1_at up kinase dystroglycan 1 CfaAffx.17467.1.S1_at up Moloney leukemia virus CfaAffx.1982.1.S1_s_at up 10-like 1

TABLE 14 Genes associated with Cellular Compromise Direction of expression Annotation Probe H v. P neuroregulin 1 CfaAffx.10523.1.S1_s_at down fibronectin 1 Cfa.3707.3.S1_s_at down macrophage receptor with Cfa.15713.1.A1_at down collagenous structure xanthine dehydrogenase CfaAffx.9452.1.S1_s_at down bactericidal permeability CfaAffx.14056.1.S1_s_at down increasing protein phospholipase C, beta 1 Cfa.10853.1.A1_at down hemoglobin epsilon 1 CfaAffx.10240.1.S1_s_at up

TABLE 15 Genes associated with various functions Direction of expression Annotation Probe H v. P CCR4-NOT transcription complex, subunit 10 Cfa.2403.1.A1_at up ubiquitin carboxy-terminal hydrolase L5 Cfa.20277.1.S1_at up SH3-domain GBR2-like 3 Cfa.10644.1.A1_at up DEAH (Asp-Glu-Ala-His) box polypeptide 8 CfaAffx.22452.1.S1_s_at up Signal-induced proliferation-associated 1 like 2 Cfa.14345.1.A1_at up Cathepsin E CfaAffx.15966.1.S1_at up ephrin-B3 Cfa.15231.1.A1_at up Fc fragment of IgG, receptor, transporter, alpha Cfa.17806.2.S1_s_at up Chromosome 20 open reading frame 172 Cfa.9662.1.A1_at up Inositol(myo)-1(or 4) monophosphatase 2 Cfa.13029.1.A1_at up Ferrochelatase (protoporphyria) Cfa.365.3.A1_x_at up G-protein coupled receptor 158 Cfa.9162.1.A1_at up dual specificity phosphatase 19 CfaAffx.22249.1.S1_at up Ring finger protein 152 Cfa.15414.1.A1_at up Chromosome 12 open reading frame 49 Cfa.11298.1.S1_at up hemoglobin, epsilon 1 CfaAffx.10240.1.S1_s_at up Crystallin lambda 1 Cfa.4354.1.S1_a_at up Sorting nexin 6 Cfa.10261.1.S1_at up microfibrillar associated protein 5 CfaAffx.21449.1.S1_s_at up coiled-coil domain containing 46 CfaAffx.17557.1.S1_s_at up Nuclear factor I/B Cfa.4487.1.S1_at up carboxypeptidase A3 CfaAffx.13076.1.S1_at up chromosome 18, clone RP11-396D4 CfaAffx.26602.1.S1_at up coxsackie and adenovirus receptor protein CfaAffx.13148.1.S1_at up WW domain containing oxidoreductase, transcript Cfa.9201.1.A1_at up variant 4 EH domain binding protein 1-like 1 Cfa.17641.1.S1_s_at Down RP4-760G15 on chromosome 11p13 Cfa.17214.1.S1_at Down phospholipase C beta 1 (phosphoinositide-Specific) Cfa.10853.1.A1_at Down cathepsin L CfaAffx.2868.1.S1_at Down Transcription elongation factor A, 1 Cfa.12580.1.S1_s_at Down glypican 6 Cfa.9523.1.A1_at Down Hypothetical protein FLJ21062 Cfa.1933.2.A1_at Down G-protein coupled receptor 101 CfaAffx.12632.1.S1_at Down Leucine-rich repeat kinase 2 CfaAffx.15613.1.S1_s_at Down Six transmembrane epithelial anitgen of the Cfa.9430.1.A1_at Down prostate 2 KIAA1074 protein Cfa.12143.1.A1_at down LOC284395 Cfa.4802.1.S1_at down elastin microfibril interfacer 2 CfaAffx.28185.1.S1_at down Sulfatase 2 CfaAffx.17034.1.S1_s_at down IBR domain containing 2 Cfa.1882.1.A1_at down Leucyl/cystinyl aminopeptidase CfaAffx.12483.1.S1_s_at down acyltransferase like 1 CfaAffx.14833.1.S1_at down NAD kinase CfaAffx.29324.1.S1_at down Immunoglobulin heavy constant alpha 2 Cfa.4556.3.A1_x_at down transcription factor EC (TFEC), transcript Cfa.1175.1.A1_s_at down variant 2 Acyl-CoA synthetase short-chain family CfaAffx.12483.1.S1_at down member 1 Syntaxin binding protein 6 Cfa.9054.1.A1_at down Opioid growth factor receptor-like 1 Cfa.583.1.S1_at down None Cfa.10106.1.A1_at down None Cfa.4556.3.A1_s_at down ELK/RAB6-interacting/CAST family member 2 Cfa.21214.1.S1_at down adipsin/complement factor D precursor Cfa.21381.1.S1_s_at down Hypothetical protein FLJ22662 CfaAffx.20271.1.S1_at down solute carrier family 2 (facilitated glucose Cfa.7132.1.A1_at down transporter), member 9 Homogentisate 1,2 dioxygenase CfaAffx.9076.1.S1_s_at down serpin peptidase inhibitor, clade B (ovalbumin), CfaAffx.1043.1.S1_s_at down member 10 None Cfa.13203.1.S1_at down Fibrinogen-like 2 CfaAffx.7369.1.S1_s_at down None Cfa.12500.1.A1_at down None Cfa.4556.2.S1_s_at down None Cfa.4555.1.S1_s_at down None Cfa.280.1.S1_at down Lymphocyte antigen 6 CfaAffx.1839.1.S1_at down Neuronal PAS domain protein 3 Cfa.12905.1.A1_a_at down

Gene expression profiles from puppies fed Composition H or P from weaning to one year of age are obtained and compared. Microarray data indicate that, at a minimum of 1.5 fold change, 99 genes are differentially expressed in the two study groups.

Genes associated with immune activation are down-regulated in puppies fed Composition H when compared to puppies fed Composition P, which suggests improved immune system function (Table 9).

Genes associated with lipid metabolism are down-regulated in puppies fed Composition H when compared to puppies fed Composition P, which suggests reduced lipid processing (Table 11).

Genes associated with cardiovascular development are also down-regulated in puppies fed Composition H when compared to puppies fed Composition P, which suggests enhanced cardiovascular health (Table 12).

Genes associated with skeletal muscular disorders are down-regulated and genes associated with muscle contraction/function are up-regulated in puppies fed Composition H when compared to puppies fed Composition P, which suggests reduced skeletal disorder risk and improved muscle contraction (Table 13).

Genes associated with cellular compromise are down-regulated in puppies fed Composition H when compared to puppies fed Composition P, which suggests reduced cellular damage (Table 14).

Genes known to have an association with cancer are down-regulated in puppies fed Composition H when compared to puppies fed Composition P, which may suggest reduced cancer susceptibility. (Table 10).

As discussed above, genetic data such as these indicate that the nutritional benefits of the compositions of the present invention include the beneficial modification of gene expression in the animal such that there is an overall enhancement in the development of the animal. In addition, the beneficial modification of gene expression may also result in a decrease in the incidence of disease in the animal due to an inhibition in expression of disease related genes and/or an increase in the expression of genes which play a role in disease prevention. 

1. A pet food composition comprising: about 5 to about 70% protein, about 0.5 to about 1.6% methionine, about 50 to about 200 ppm manganese, about 0.1 to about 0.5% DHA. about 0.1 to about 0.7% EPA. about 1200 to about 7500 ppm choline, about 1000 to about 2000 ppm taurine, about 2.5 to about 6% linoleic acid, about 1 to about 3% total n-3 fatty acids, about 50 to about 1200 IU/kg vitamin E. about 50 to about 500 ppm vitamin C, about 50 to about 500 ppm carnitine, and about 2.5 to about 7 g lysine/1000 kcal.
 2. The composition of claim 1 comprising: 0 to about 90% by weight of carbohydrates: about 20% to about 60% by weight of protein; about 2% to about 50% by weight of fat; about 0.1% to about 20% by weight of total dietary fiber; and 0 to about 15% by weight of vitamins, minerals, and other nutrients
 3. The composition of claim 1 comprising about 0.1% to about 0.4% DHA.
 4. The composition of claim 1 comprising about 100 ppm to about 500 ppm carnitine.
 5. The composition of claim 1 comprising about 2.5 g/1000 kcal to about 7 a/1000 kcal lysine.
 6. The composition of claim 1 comprising about 0.1% to about 0.6% EPA.
 7. The composition of claim 1 comprising about 50 ppm to about 150 ppm manganese.
 8. The composition of claim 1 comprising about 0.8% to about 1.6% methionine.
 9. A method to regulate gene expression in a canine comprising administering to the canine or to the mother of the canine while the canine is in utero a composition according to claim
 1. 10. The method of claim 9 wherein the canine is a puppy.
 11. The method of claim 9 wherein the canine is born of a dam fed the composition during pregnancy.
 12. The method of claim 10 wherein the puppy is in utero.
 13. The method of claim 11 wherein the dam is fed the composition prior to pregnancy.
 14. The method of claim 11 wherein the dam is fed the composition for a majority of the pregnancy duration.
 15. The method of claim 11 wherein the dam is fed the composition prior to and during pregnancy.
 16. The method of claim 10 wherein the puppy is fed the composition prior to weaning.
 17. The method of claim 10 wherein the puppy is fed the composition post weaning.
 18. The method of claim 17 wherein the puppy is fed the composition substantially exclusively.
 19. The method of claim 9 wherein an effective amount of the composition is administered to the canine.
 20. The method claim 9 wherein the composition is administered to the canine for an effective amount of time.
 21. The method of claim 20 wherein the composition is administered to the canine for at least one year post partum or one year post weaning.
 22. The method claim 9 wherein the gene is selected from those listed in Tables 2-15.
 23. A method to cause a beneficial modification in the expression of any one or more genes provided in Tables 2-5 in an animal, for any one or more biological conditions, pathways or disease states described in Tables 2-15, comprising administering an effective amount of a composition according claim 1 to the animal, either directly to the animal or to the dam of the animal while the animal is in utero. 